Evaluate gene sets by cell type-specific gene expression

Setup

Load R libraries

library(data.table)
library(ggplot2)
library(ggpubr)
library(tidyr)
library(limma)
library(stringr)

theme_set(theme_classic())

cell_type_name = params$cell_type_name
graph_weight = params$graph_weight

cell_type_name

## [1] "Micro-PVM"

graph_weight

## [1] "2.0"

Check the expression of each gene set in each brain-related cell type

Read in gene info and gene set assignments

file_tag = sprintf("%s_%s", cell_type_name, graph_weight)

assayed_genes = scan(sprintf("output/gene_list_%s.txt", file_tag), 
                     what = character(), sep="\n")

length(assayed_genes)

## [1] 2000

gene_sets = scan(sprintf("output/name_s_%s.txt", file_tag), 
                 what = character(), sep="\n")

gene_sets = sapply(gene_sets, strsplit, split=",")
n_genes   = sapply(gene_sets, length)
names(n_genes) = NULL
summary(n_genes)

##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##    35.0    38.0    39.0    39.1    41.0    42.0

length(n_genes)

## [1] 40

sort(n_genes)

##  [1] 35 35 37 37 37 37 37 37 38 38 38 38 38 38 39 39 39 39 39 39 39 39 39 39 39
## [26] 39 40 41 41 41 41 41 41 41 41 41 41 42 42 42

Find gene symbols using the alias2Symbol function from limma.

a2s = rep(NA, length(assayed_genes))
for(i in 1:length(assayed_genes)){
  gi = assayed_genes[i]
  ai = alias2Symbol(gi)
  if(length(ai) > 1){
    print(gi)
    print(ai)
  }
  a2s[i] = ai[1]
}

table(is.na(a2s))

## 
## FALSE  TRUE 
##  1739   261

table(a2s == assayed_genes, useNA = 'ifany')

## 
## FALSE  TRUE  <NA> 
##    21  1718   261

gene_info = data.table(sym_in_data = assayed_genes, sym_limma = a2s)

gene_info[sym_in_data != sym_limma,]

##     sym_in_data   sym_limma
##  1:       LRRC6     DNAAF11
##  2:    C11orf49      CSTPP1
##  3:   LINC00476 ERCC6L2-AS1
##  4:  HNRNPA1P48   HNRNPA1L3
##  5:  ZRANB2-AS2   ZRANB2-DT
##  6:   LINC00271     AHI1-DT
##  7:    RFX3-AS1     RFX3-DT
##  8:   LINC00884  ATP13A3-DT
##  9:   FBXO30-DT    EPM2A-DT
## 10:   LINC00894    EOLA2-DT
## 11:   COX10-AS1    COX10-DT
## 12:   LINC01184  SLC12A2-DT
## 13: FAM198B-AS1  GASK1B-AS1
## 14:     C5orf17   LINC02899
## 15: C8orf37-AS1 CFAP418-AS1
## 16:   LINC01146       HISLA
## 17:      BTBD11       ABTB3
## 18:       H2BU1      H2BC26
## 19:      SKIV2L       SKIC2
## 20:     FAM155A       NALF1
## 21:  CTB-41I6.2   PIK3R5-DT
##     sym_in_data   sym_limma

gene_info[, gene_symbol := sym_in_data]
gene_info[which(sym_in_data != sym_limma & (gene_symbol != "MT-CO2")), 
                gene_symbol := sym_limma]

dim(gene_info)

## [1] 2000    3

gene_info[1:5,]

##    sym_in_data sym_limma gene_symbol
## 1:        CFTR      CFTR        CFTR
## 2:        ICA1      ICA1        ICA1
## 3:        PDK4      PDK4        PDK4
## 4:       CALCR     CALCR       CALCR
## 5:       ABCB4     ABCB4       ABCB4

t1 = table(gene_info$gene_symbol)
table(t1)

## t1
##    1 
## 2000

Read in cell type-specific expression data

Gene set annotations (by gene symbols) were downloaded from MSigDB website.

ct = fread("../Annotation/rna_single_cell_type.tsv.gz")
dim(ct)

## [1] 1587110       4

ct[1:5,]

##               Gene Gene name             Cell type  nTPM
## 1: ENSG00000000003    TSPAN6            Adipocytes 149.5
## 2: ENSG00000000003    TSPAN6 Alveolar cells type 1   6.1
## 3: ENSG00000000003    TSPAN6 Alveolar cells type 2  10.5
## 4: ENSG00000000003    TSPAN6            Astrocytes  13.9
## 5: ENSG00000000003    TSPAN6               B-cells   1.5

length(unique(ct$`Cell type`))

## [1] 79

table(ct$`Cell type`)

## 
##                      Adipocytes           Alveolar cells type 1 
##                           20090                           20090 
##           Alveolar cells type 2                      Astrocytes 
##                           20090                           20090 
##                         B-cells             Basal keratinocytes 
##                           20090                           20090 
##           Basal prostatic cells         Basal respiratory cells 
##                           20090                           20090 
## Basal squamous epithelial cells                   Bipolar cells 
##                           20090                           20090 
##          Breast glandular cells      Breast myoepithelial cells 
##                           20090                           20090 
##                  Cardiomyocytes                  Cholangiocytes 
##                           20090                           20090 
##                      Club cells           Collecting duct cells 
##                           20090                           20090 
##        Cone photoreceptor cells                Cytotrophoblasts 
##                           20090                           20090 
##                 dendritic cells              Distal enterocytes 
##                           20090                           20090 
##            Distal tubular cells                    Ductal cells 
##                           20090                           20090 
##                Early spermatids      Endometrial ciliated cells 
##                           20090                           20090 
##       Endometrial stromal cells               Endothelial cells 
##                           20090                           20090 
##           Enteroendocrine cells                 Erythroid cells 
##                           20090                           20090 
##              Excitatory neurons        Exocrine glandular cells 
##                           20090                           20090 
##       Extravillous trophoblasts                     Fibroblasts 
##                           20090                           20090 
##   Gastric mucus-secreting cells     Glandular and luminal cells 
##                           20090                           20090 
##                    granulocytes                 Granulosa cells 
##                           20090                           20090 
##                     Hepatocytes                  Hofbauer cells 
##                           20090                           20090 
##                Horizontal cells              Inhibitory neurons 
##                           20090                           20090 
##         Intestinal goblet cells                       Ionocytes 
##                           20090                           20090 
##                   Kupffer cells                Langerhans cells 
##                           20090                           20090 
##                 Late spermatids                    Leydig cells 
##                           20090                           20090 
##                     Macrophages                     Melanocytes 
##                           20090                           20090 
##                Microglial cells                       monocytes 
##                           20090                           20090 
##           Mucus glandular cells               Muller glia cells 
##                           20090                           20090 
##                        NK-cells Oligodendrocyte precursor cells 
##                           20090                           20090 
##                Oligodendrocytes      Pancreatic endocrine cells 
##                           20090                           20090 
##                    Paneth cells               Peritubular cells 
##                           20090                           20090 
##                    Plasma cells       Prostatic glandular cells 
##                           20090                           20090 
##            Proximal enterocytes          Proximal tubular cells 
##                           20090                           20090 
##      Respiratory ciliated cells         Rod photoreceptor cells 
##                           20090                           20090 
##             Salivary duct cells                   Schwann cells 
##                           20090                           20090 
##          Serous glandular cells                   Sertoli cells 
##                           20090                           20090 
##               Skeletal myocytes             Smooth muscle cells 
##                           20090                           20090 
##                   Spermatocytes                   Spermatogonia 
##                           20090                           20090 
##       Squamous epithelial cells        Suprabasal keratinocytes 
##                           20090                           20090 
##            Syncytiotrophoblasts                         T-cells 
##                           20090                           20090 
##                     Theca cells         Thymic epithelial cells 
##                           20090                           20090 
##          Undifferentiated cells 
##                           20090

cell_group = fread("../Annotation/rna_single_cell_type_brain.tsv")
dim(cell_group)

## [1] 16  2

cell_group[1:2,]

##             Cell_type Cell_group
## 1: Excitatory neurons   Neuronal
## 2: Inhibitory neurons   Neuronal

ct = ct[`Cell type` %in% cell_group$Cell_type,]
table(ct$`Cell type`)

## 
##                      Astrocytes                         B-cells 
##                           20090                           20090 
##                   Bipolar cells        Cone photoreceptor cells 
##                           20090                           20090 
##              Excitatory neurons                Horizontal cells 
##                           20090                           20090 
##              Inhibitory neurons                Microglial cells 
##                           20090                           20090 
##               Muller glia cells Oligodendrocyte precursor cells 
##                           20090                           20090 
##                Oligodendrocytes                    Plasma cells 
##                           20090                           20090 
##         Rod photoreceptor cells                   Schwann cells 
##                           20090                           20090 
##                         T-cells 
##                           20090

Check gene expression for each gene set

dim(gene_info)

## [1] 2000    3

for(k in 1:length(gene_sets)){
  if(length(gene_sets[[k]]) < 10) { next }
  
  print(k)
  set_k = paste0("set_", k)
  print(gene_sets[[k]])
  
  genes = gene_info[sym_in_data %in% gene_sets[[k]], gene_symbol]

  n_genes = sum(genes %in% ct$`Gene name`)
  print(sprintf("found %d genes.", n_genes))

  if(n_genes == 0) { next }

  df = ct[`Gene name` %in% genes,]
  dim(df)
  df[1:2,]
  
  stopifnot(all(str_to_lower(df$`Cell type`) %in% 
                  str_to_lower(cell_group$Cell_type)))
  
  mat1 = match(str_to_lower(df$`Cell type`), 
               str_to_lower(cell_group$Cell_type))
  
  df = cbind(df, cell_group[mat1,])
  df[1:2,]
  
  df$Cell_type = factor(df$Cell_type, levels = cell_group$Cell_type)
  df$Cell_group = factor(df$Cell_group, 
                         levels = unique(cell_group$Cell_group))
  
  p1 = ggplot(df, aes(x=Cell_type, y=log10(nTPM + 0.1), fill=Cell_group)) + 
    geom_boxplot() + xlab("Cell type") + ggtitle(set_k) + 
    theme(axis.text.x = element_text(angle = 45, hjust = 1)) + 
    scale_fill_brewer(palette="RdBu")

  print(p1)
}

## [1] 1
##  [1] "CEACAM1"       "HAMP"          "DUOX1"         "RAB40B"       
##  [5] "FOLR2"         "ADGRG2"        "FLJ40194"      "DLEU7"        
##  [9] "FAM177B"       "HNRNPA1P48"    "EDNRB-AS1"     "LINC01375"    
## [13] "ENTPD1-AS1"    "SLC8A1-AS1"    "RP11-142M10.2" "SRGAP2-AS1"   
## [17] "AC092431.3"    "RNASEH2B-AS1"  "RP11-353M9.1"  "RP11-666F17.1"
## [21] "RP11-796E2.4"  "FAM198B-AS1"   "RP11-360F5.1"  "AC006160.5"   
## [25] "RP11-281P23.2" "RP11-238K6.1"  "RP11-649G15.2" "RP11-452H21.1"
## [29] "RP11-513G19.1" "RP11-486A14.2" "RP11-136F16.1" "RP11-370I10.2"
## [33] "RP11-517O13.1" "ABHD15-AS1"    "RP11-264E23.4" "RP11-7F3.1"   
## [37] "AC009166.9"    "RP11-56I23.2"  "EME2"         
## [1] "found 9 genes."

## [1] 2
##  [1] "OSBPL6"   "P3H2"     "GCNT2"    "TENT5A"   "RALGPS2"  "NRN1"    
##  [7] "MIS18BP1" "KCNMB1"   "AIG1"     "SLC25A25" "MAGI1"    "PTPN14"  
## [13] "KCNMA1"   "TIAM1"    "TMEM169"  "PLEKHA7"  "NXN"      "S100Z"   
## [19] "MBOAT1"   "SH3RF3"   "NCKAP5"   "APOO"     "PLEKHA5"  "RASSF2"  
## [25] "MICU1"    "DENND1A"  "SLC35E1"  "ZBTB46"   "STARD13"  "DENND4C" 
## [31] "SLC12A6"  "SRSF12"   "AGAP1"    "SLC43A2"  "FAM110B"  "TANC2"   
## [37] "SIPA1L1" 
## [1] "found 37 genes."

## [1] 3
##  [1] "ABCB4"          "ARL5C"          "AZIN2"          "RASGEF1C"      
##  [5] "TMEM163"        "GHRL"           "GASK1B"         "ADAMTS15"      
##  [9] "MICOS10"        "MARCHF3"        "PLCXD3"         "KBTBD12"       
## [13] "AC007879.5"     "RP1-30E17.2"    "CCDC26"         "AC002539.1"    
## [17] "LINC02642"      "COX10-AS1"      "LINC01141"      "KCNMB2-AS1"    
## [21] "LINC02008"      "RP11-246A10.1"  "XACT"           "LINC02057"     
## [25] "LINC01091"      "AC008697.1"     "LINC01094"      "RP11-745L13.2" 
## [29] "CTC-575N7.1"    "MAILR"          "SMIM35"         "RP11-554D14.6" 
## [33] "LINC02444"      "RP11-588H23.3"  "RP11-72M17.1"   "RP11-399K21.11"
## [37] "LINC02712"      "LINC01374"      "RP11-692P14.1"  "RP11-321P16.3" 
## [41] "RP1-236J16.3"  
## [1] "found 13 genes."

## [1] 4
##  [1] "BEX1"         "ENPP3"        "SLC9B1"       "GPR85"        "TCERG1L"     
##  [6] "WEE2-AS1"     "AC011288.2"   "COA6-AS1"     "LINC00996"    "ZNF528-AS1"  
## [11] "TENM1"        "FGF14"        "ATP8A2"       "STXBP5L"      "TENM2"       
## [16] "CNTN5"        "ADGRL3"       "ZNF385D"      "SPOCK1"       "AK5"         
## [21] "NCAM2"        "CAMK2N1"      "GABRB1"       "CSMD3"        "LRFN5"       
## [26] "NEGR1"        "FUT9"         "KCTD16"       "FLRT2"        "LSAMP"       
## [31] "PTPRT"        "TAFA2"        "LINC00632"    "FAM155A"      "MEG3"        
## [36] "RP11-191L9.4" "AC093843.1"   "SHISA9"       "RP11-384F7.2" "AGBL1"       
## [41] "IQCJ-SCHIP1" 
## [1] "found 30 genes."

## [1] 5
##  [1] "RBL1"         "PRTFDC1"      "DAAM1"        "ARHGEF18"     "ARSB"        
##  [6] "LRRC6"        "ZSCAN5A"      "MTHFS"        "RALGPS1"      "MAMDC2"      
## [11] "ARHGAP42"     "CDYL2"        "LCLAT1"       "SCAI"         "LINC00476"   
## [16] "C5orf64"      "FIGN"         "KIAA0825"     "CENPP"        "SCOC-AS1"    
## [21] "RANBP17"      "ATP6AP1L"     "LIN52"        "SLC16A1-AS1"  "RP11-120D5.1"
## [26] "RORA-AS1"     "LINC00506"    "SNX25"        "E2F3"         "GABRG2"      
## [31] "HELLS"        "NR6A1"        "GREM1"        "FRMD3"        "CDH4"        
## [36] "SERTAD2"      "SYCP2"        "RP5-864K19.4" "CYP1B1-AS1"   "HCG17"       
## [41] "C2orf27A"    
## [1] "found 28 genes."

## [1] 6
##  [1] "CELSR3"               "ZNF365"               "RBMS3"               
##  [4] "CLSTN2"               "NRG2"                 "PRICKLE2"            
##  [7] "ARHGEF3"              "RANBP3L"              "ADGRV1"              
## [10] "FSTL5"                "HPSE2"                "LRRC3B"              
## [13] "POTEG"                "CACNA1E"              "ZNF521"              
## [16] "LINC00970"            "XKR9"                 "AC023469.1"          
## [19] "ROR1-AS1"             "SATB1-AS1"            "LINC01435"           
## [22] "RP11-147G16.1"        "RP11-154D17.1"        "AC013463.2"          
## [25] "AC002066.1"           "CTC-340A15.2"         "USP2-AS1"            
## [28] "RP11-696N14.1"        "RP1-179N16.6"         "LINC01609"           
## [31] "RP11-661A12.5"        "RMST"                 "RP11-20D14.3"        
## [34] "RP11-396B14.2"        "MTRNR2L12"            "RMRP_ENSG00000269900"
## [37] "LINC00551"            "CH507-513H4.1"        "CH507-528H12.1"      
## [40] "RP11-596C23.6"        "RP4-799O8.1"          "RP11-398J12.1"       
## [1] "found 17 genes."

## [1] 7
##  [1] "SYNDIG1"       "PLAT"          "FAM149A"       "TMEM156"      
##  [5] "ARMH4"         "RP11-493L12.4" "ARHGAP6"       "FSTL4"        
##  [9] "DDX3Y"         "PILRA"         "TGFB2"         "GRK3"         
## [13] "ITGB8"         "SERPINE1"      "BICRAL"        "PADI2"        
## [17] "OGFRL1"        "CDH26"         "TIAM2"         "SLC2A13"      
## [21] "DHRS13"        "NCMAP"         "GLDN"          "CCDC73"       
## [25] "NHEJ1"         "ZNF846"        "CYRIA"         "ZDBF2"        
## [29] "GCC2-AS1"      "AC025171.1"    "LNCAROD"       "MYO16-AS1"    
## [33] "FMN1"          "RP11-351A11.1" "RP11-111A21.1" "RP11-707P17.1"
## [37] "RP11-358F13.1" "RP11-404C6.6"  "RP11-452F19.4"
## [1] "found 28 genes."

## [1] 8
##  [1] "SIGLEC1"       "PCSK1N"        "MAP3K8"        "FLVCR2"       
##  [5] "F13A1"         "ENOSF1"        "IFI44L"        "CH25H"        
##  [9] "HERC6"         "UBE2Q2"        "FHAD1"         "TMEM44"       
## [13] "ADAMTS19"      "ADGRA3"        "BEX3"          "MT1E"         
## [17] "OLR1"          "ODF3B"         "H2BC4"         "MX2"          
## [21] "H2BC18"        "TMSB4X"        "MS4A4E"        "RP11-123B3.2" 
## [25] "RP5-1101C3.1"  "ARHGAP8"       "LINC01258"     "LINC02196"    
## [29] "ZNF10"         "RP1-71H24.1"   "OVCH1-AS1"     "RP11-323I15.5"
## [33] "LINC01572"     "RP11-386I14.4" "H2BC8"         "H2AC8"        
## [37] "RP11-736I24.5" "PLXNC1"       
## [1] "found 28 genes."

## [1] 9
##  [1] "CALCR"                     "ZNF532"                   
##  [3] "MBNL3"                     "OPHN1"                    
##  [5] "MS4A4A"                    "ADGRG6"                   
##  [7] "LDAH"                      "MTERF1"                   
##  [9] "PIGC"                      "LRIG1"                    
## [11] "PSTPIP2"                   "PID1"                     
## [13] "RAB28"                     "PUS10"                    
## [15] "TMEM144"                   "DNAJC24"                  
## [17] "WDR25"                     "SDHAF3"                   
## [19] "PRDX6-AS1"                 "MAMDC2-AS1"               
## [21] "ZNF433-AS1"                "LINC00630"                
## [23] "RPL34-DT"                  "LINC01278"                
## [25] "RP11-195C7.1"              "LINC02432"                
## [27] "PVT1"                      "RP11-130F10.1"            
## [29] "LIX1-AS1"                  "LINC01605_ENSG00000253161"
## [31] "LINC01146"                 "DISC1FP1"                 
## [33] "EIF1B-AS1"                 "RP11-323F24.5"            
## [35] "RP4-545L17.11"             "PARP8"                    
## [37] "IL15"                      "TMEM65"                   
## [39] "APLF"                      "KCNE1"                    
## [41] "ZNF407"                   
## [1] "found 24 genes."

## [1] 10
##  [1] "TPD52"      "RPL3"       "RPL18A"     "RPL19"      "RPL34"     
##  [6] "RPL24"      "ATP5F1E"    "FGF13"      "RPS24"      "PRDM5"     
## [11] "RPS2"       "RPS11"      "RPL11"      "SPAG16"     "RPL32"     
## [16] "FAU"        "BEND6"      "ATG10"      "RPL26"      "ELAVL4"    
## [21] "MRPL1"      "RPL38"      "RPLP2"      "RPS23"      "SPATS2L"   
## [26] "CPNE4"      "RPL12"      "RPL23A"     "RPL39"      "AIF1"      
## [31] "DOK6"       "SPOCK2"     "SLC1A2"     "ZMAT4"      "LPL"       
## [36] "ADARB1"     "LILRB3"     "SLC5A4-AS1"
## [1] "found 37 genes."

## [1] 11
##  [1] "DERA"      "SNX24"     "ITGA6"     "POLA1"     "MID1"      "SUSD1"    
##  [7] "APBA1"     "MAP2K6"    "WLS"       "AKAP7"     "SLC10A7"   "DTD1"     
## [13] "METTL25"   "LANCL2"    "DPH6"      "NPL"       "IRF8"      "MMS22L"   
## [19] "NUBPL"     "SAMSN1"    "BACH1"     "C1QC"      "TNFRSF13C" "FILIP1L"  
## [25] "SLC35G2"   "C1QA"      "PTPN2"     "RTTN"      "PROS1"     "CCDC7"    
## [31] "HGF"       "FDFT1"     "HACE1"     "KLHL24"    "COL5A1"    "FNBP1L"   
## [37] "GOLIM4"   
## [1] "found 37 genes."

## [1] 12
##  [1] "NEXMIF"        "NAV3"          "CASS4"         "PLCL1"        
##  [5] "GARNL3"        "GIPC2"         "UNC80"         "TSPAN7"       
##  [9] "CACNA1D"       "RNF180"        "CCDC171"       "NAV2"         
## [13] "ZNF608"        "MACROD2"       "KCNIP1"        "ERC2"         
## [17] "COL25A1"       "ALOX12-AS1"    "LINC00539"     "RP11-535M15.1"
## [21] "STX18-AS1"     "LINC02232"     "MRPS30-DT"     "RP4-809F18.1" 
## [25] "RP11-370I10.6" "RP11-622O11.6" "COPG2IT1"      "RP11-640F22.1"
## [29] "RP11-320L2.1"  "DOCK3"         "CUX2"          "WDR45B"       
## [33] "KCND3"         "DPP10"         "ANKS1B"        "KCNIP4"       
## [37] "AIDA"          "RYR2"          "SNHG14"       
## [1] "found 26 genes."

## [1] 13
##  [1] "MCF2L2"   "CYFIP2"   "CST3"     "STS"      "ABCC4"    "DOCK10"  
##  [7] "BCAS3"    "FOXO1"    "BTG2"     "ANO10"    "ARHGAP25" "B2M"     
## [13] "BTD"      "SERPINB9" "XKR6"     "DYNC2H1"  "RPL41"    "RORA"    
## [19] "SLC1A3"   "DOCK9"    "PRKAG2"   "RAPGEF1"  "PTPRE"    "SSH2"    
## [25] "SDK1"     "MGAT5"    "FMNL2"    "RUNX1"    "CLASP2"   "OXR1"    
## [31] "LDLRAD4"  "GPHN"     "CEBPB"    "CHD2"     "BAIAP2"   "MYO1D"   
## [37] "PCDH9"    "GDI1"     "NEAT1"   
## [1] "found 38 genes."

## [1] 14
##  [1] "TNFRSF21" "JARID2"   "ARAP2"    "CPSF1"    "GRAMD4"   "PPP1R15A"
##  [7] "CEP170B"  "TBL1X"    "INTS6"    "HSF4"     "UBE2R2"   "DNAJC12" 
## [13] "DCUN1D4"  "BBX"      "CYTIP"    "TSHZ3"    "MGAT1"    "PHF21A"  
## [19] "IQGAP2"   "GFOD1"    "GNA12"    "THRB"     "RPP38"    "CAMK4"   
## [25] "RASSF3"   "ASAP1"    "RASA2"    "CDC42SE2" "SLMAP"    "STXBP5"  
## [31] "PCDH7"    "SH3PXD2B" "CMSS1"    "ARL4C"    "RALGAPA2" "IARS1"   
## [37] "ZNF277"   "EFCAB2"   "ZSCAN31" 
## [1] "found 39 genes."

## [1] 15
##  [1] "LRRC74A"    "MEIS1"      "ZNF707"     "HECW1"      "PKD1"      
##  [6] "NCDN"       "PTPRN"      "ITPKC"      "PCSK5"      "FLT1"      
## [11] "EPHA4"      "KDM5B"      "NR4A3"      "ZC4H2"      "AFDN"      
## [16] "EMILIN2"    "RAMP1"      "MACROD1"    "MICAL2"     "KCNK1"     
## [21] "CRIM1"      "NPAS3"      "CACNA2D1"   "PTPRN2"     "SORCS3"    
## [26] "PALM2AKAP2" "FGF17"      "SPTBN4"     "UNC5C"      "TSHZ2"     
## [31] "NELL2"      "ZBTB7C"     "PBX1"       "MIB2"       "SLC48A1"   
## [36] "MTRNR2L1"   "GRIN2B"    
## [1] "found 37 genes."

## [1] 16
##  [1] "PRKCQ"      "FOXP2"      "ATF5"       "XIST"       "GCLC"      
##  [6] "GCLM"       "PRKCH"      "WWC3"       "ZFAT"       "MYO9A"     
## [11] "ARHGAP15"   "ANKRD12"    "ADAP1"      "MEGF9"      "FOXP1"     
## [16] "SEM1"       "KIAA0513"   "CAMKMT"     "FER"        "RASGRP3"   
## [21] "MERTK"      "JAZF1"      "ADK"        "ST3GAL2"    "EPB41"     
## [26] "FBXO27"     "NEK10"      "MTSS1"      "MALT1"      "FUT10"     
## [31] "RESF1"      "SLC35E3"    "SAMD12"     "CSMD1"      "MAML2"     
## [36] "NPIPB15"    "CARD11"     "SOGA3"      "AC092835.2"
## [1] "found 37 genes."

## [1] 17
##  [1] "ADGRD1"        "PDE10A"        "NEURL2"        "BANK1"        
##  [5] "ADAMTS3"       "UCN"           "PGBD5"         "TMEM151B"     
##  [9] "HDAC4-AS1"     "RP11-445F6.2"  "SMCR5"         "LINC01515"    
## [13] "LINC01277"     "RP3-525N10.2"  "LINC00271"     "LINC02884"    
## [17] "AC007682.1"    "RP11-142A5.1"  "AC073115.6"    "BDNF-AS"      
## [21] "LINC02211"     "RP11-115J16.1" "C5orf17"       "RP11-673E1.1" 
## [25] "LINC02055"     "FAM66D"        "MIR100HG"      "PRANCR"       
## [29] "CTD-2336H13.2" "LINC02073"     "CCDC28A-AS1"   "RP11-413N10.3"
## [33] "CERNA2"        "RP11-221G19.1" "LINC02885"     "RP11-237N2.1" 
## [37] "RP11-38B6.1"   "RP13-52K8.2"  
## [1] "found 8 genes."

## [1] 18
##  [1] "OSBPL5"                  "SNCAIP"                 
##  [3] "MGLL"                    "RPH3A"                  
##  [5] "GDAP1"                   "CD69"                   
##  [7] "PDE4D"                   "ZRANB3"                 
##  [9] "CHN1"                    "CALY"                   
## [11] "EFCAB11"                 "RNF157"                 
## [13] "NRGN"                    "ABCA5"                  
## [15] "CPLX1"                   "KCNMB2"                 
## [17] "ALG1L9P_ENSG00000248671" "CEROX1"                 
## [19] "ADAM22"                  "VCAN"                   
## [21] "PDE4A"                   "KCNAB2"                 
## [23] "RAB27A"                  "ZNF586"                 
## [25] "NCS1"                    "SASH1"                  
## [27] "HPCAL1"                  "SH3BP5"                 
## [29] "SNAP25"                  "PAM"                    
## [31] "MSI2"                    "STARD9"                 
## [33] "KALRN"                   "MSRA"                   
## [35] "CADM1"                   "PDE4B"                  
## [37] "KAZN"                    "UNC13B"                 
## [39] "MICAL3"                 
## [1] "found 37 genes."

## [1] 19
##  [1] "ETV1"      "SCMH1"     "IGF1"      "PER3"      "APBB1IP"   "IL1A"     
##  [7] "IL1B"      "IL6ST"     "SLC22A23"  "TRPC1"     "MLIP"      "COPG2"    
## [13] "NLRP3"     "KIF26B"    "SFMBT1"    "TMEM52B"   "DTWD2"     "DENND5B"  
## [19] "DLEU1"     "SLC8A1"    "PRKN"      "SFMBT2"    "MBD5"      "LTC4S"    
## [25] "LIPE-AS1"  "MIR99AHG"  "MATK"      "RNASET2"   "RBFOX1"    "PDGFB"    
## [31] "LIFR"      "HPCAL4"    "SLC6A8"    "SLC2A5"    "FAT3"      "RBFOX3"   
## [37] "TNFRSF10C" "PCGF5"    
## [1] "found 35 genes."

## [1] 20
##  [1] "ZFP64"         "EFR3B"         "EPDR1"         "TXNDC16"      
##  [5] "PARD3B"        "GALNT12"       "IFT43"         "SIRPD"        
##  [9] "FBN2"          "TEX9"          "LINC00467"     "DISP1"        
## [13] "CLIC2"         "MAP3K7CL"      "AIM2"          "ATF7IP2"      
## [17] "TMC7"          "SPTLC3"        "RAB39A"        "FSIP2"        
## [21] "LEKR1"         "LINC01356"     "AC097721.2"    "RP5-1198O20.4"
## [25] "FSIP2-AS1"     "RP11-634B7.4"  "CDKN2B-AS1"    "LINC00968"    
## [29] "STARD4-AS1"    "RP11-120A1.1"  "RP11-10H3.1"   "MIR3142HG"    
## [33] "RHOXF1-AS1"    "LINC02666"     "RP1-111C20.3"  "GALNT18"      
## [37] "ARHGEF25"      "CPEB2-DT"      "CTB-41I6.2"   
## [1] "found 22 genes."

## [1] 21
##  [1] "ERCC8"   "OXCT1"   "ALDOC"   "CCDC18"  "DSTN"    "PIGK"    "IER2"   
##  [8] "BACE2"   "ABAT"    "CDK14"   "CDK17"   "TGFBR3"  "PGM1"    "NPDC1"  
## [15] "TPI1"    "SOD2"    "PAPOLG"  "HSPH1"   "CAMK1"   "DNAJB2"  "UACA"   
## [22] "CPNE8"   "MSN"     "MCPH1"   "CFDP1"   "PTMS"    "PCNT"    "GLRX"   
## [29] "AGFG1"   "FAM20C"  "ZDHHC20" "LIMK2"   "COL27A1" "HSPA1B"  "PPME1"  
## [1] "found 35 genes."

## [1] 22
##  [1] "ACKR4"         "HIVEP2"        "MAMLD1"        "HDHD5"        
##  [5] "MAP3K20"       "GADD45B"       "IL4I1"         "LILRB5"       
##  [9] "HS3ST2"        "TREM1"         "GPNMB"         "NIBAN2"       
## [13] "RASGEF1B"      "TAMALIN"       "IER5"          "ATOH8"        
## [17] "VMO1"          "ADSS1"         "ANKRD37"       "ZNF395"       
## [21] "TPRG1"         "H2BU1"         "AF064858.6"    "AS3MT"        
## [25] "FAM229A"       "LIMD1-AS1"     "DIRC3"         "DARS1-AS1"    
## [29] "RP11-47I22.3"  "AC009505.4"    "MIR155HG"      "AF064858.8"   
## [33] "SELENOP"       "LINC02698"     "CLEC5A"        "SAP30-DT"     
## [37] "MYOCOS"        "RP11-475M20.2" "CTD-2285E13.1" "RENO1"        
## [41] "RP11-134L10.2"
## [1] "found 26 genes."

## [1] 23
##  [1] "RIPOR2"        "LILRB2"        "MCTP2"         "ABCA8"        
##  [5] "MTHFD2L"       "RAB37"         "ARSJ"          "CARNMT1-AS1"  
##  [9] "PCDH9-AS2"     "AC073115.7"    "TRG-AS1"       "RP11-341N18.1"
## [13] "RP11-120L14.1" "GALNT16"       "CDH20"         "MYOM1"        
## [17] "KATNAL1"       "STN1"          "ARFGEF3"       "ADAM23"       
## [21] "MXI1"          "ATP8A1"        "PCSK2"         "PATJ"         
## [25] "BTBD11"        "PITPNC1"       "FBXO32"        "ZFYVE28"      
## [29] "JAML"          "PLPP3"         "SNED1"         "AMER2"        
## [33] "KLF13"         "TBC1D10C"      "JAKMIP2"       "ZHX2"         
## [37] "TMTC2"         "SSTR2"         "CD247"         "CCDC71L"      
## [41] "LINC01138"    
## [1] "found 33 genes."

## [1] 24
##  [1] "RASGRP2"                 "FAM50A"                 
##  [3] "ADGRL1"                  "SLC26A3"                
##  [5] "AK1"                     "DRAM1"                  
##  [7] "CCNG2"                   "PGGHG"                  
##  [9] "PXDNL"                   "LRRC4C"                 
## [11] "CLEC1A"                  "AMN1"                   
## [13] "CFAP161"                 "TNFRSF11B"              
## [15] "SEMA3E"                  "LPCAT4"                 
## [17] "LINC00910"               "LINC00862"              
## [19] "LINC02397"               "C17orf67"               
## [21] "LINC01320"               "ARL17B"                 
## [23] "KLF3-AS1"                "SGO1-AS1"               
## [25] "AC067959.1"              "LINC01762"              
## [27] "RP3-467L1.4"             "LINC02646"              
## [29] "RP11-305L7.3"            "RP11-657O9.1"           
## [31] "LINC01322"               "RP11-17A1.3"            
## [33] "RP11-79E3.2"             "RP11-81K2.1"            
## [35] "SCARNA2_ENSG00000270066" "RP11-154H23.4"          
## [37] "RP11-114N19.3"           "RP11-344F5.1"           
## [39] "AC003099.2"             
## [1] "found 18 genes."

## [1] 25
##  [1] "MPP2"     "IRAK1BP1" "SKA2"     "CNTN1"    "LRRC7"    "CTNNA2"  
##  [7] "ZFY"      "ARHGAP10" "RAPGEF4"  "CELF4"    "KCNT1"    "CPE"     
## [13] "MOB3B"    "OLFM1"    "PDZD2"    "KCNH1"    "CDH18"    "CNKSR2"  
## [19] "ME3"      "SCN3A"    "FMN2"     "SYN2"     "EDIL3"    "NLGN1"   
## [25] "CTNND2"   "DLGAP1"   "C11orf80" "CNTNAP2"  "PPM1E"    "RIMS2"   
## [31] "NRXN1"    "OPCML"    "RALYL"    "OSBP2"    "PRKG1"    "SYN3"    
## [37] "MYT1L"    "MAGI2"    "GRM7"    
## [1] "found 39 genes."

## [1] 26
##  [1] "ADAM28"  "PROCR"   "NEK11"   "CCDC170" "SMAD6"   "MED12L"  "SAMD4A" 
##  [8] "NSMAF"   "LIMCH1"  "PHLPP1"  "IRAK3"   "FKBP5"   "USP9Y"   "FOXO3"  
## [15] "ELL2"    "RUNX2"   "DOCK6"   "ZNF331"  "IRAK2"   "CCNH"    "NHSL1"  
## [22] "FAM117B" "FAM13A"  "PELI2"   "MAP3K6"  "USP53"   "NEK7"    "PDE3B"  
## [29] "OTUD1"   "LRP1B"   "PPIP5K1" "BNC2"    "H2AC6"   "GPRIN3"  "SULF2"  
## [36] "PELI1"   "CEBPD"  
## [1] "found 37 genes."

## [1] 27
##  [1] "IPCEF1"     "PEX7"       "ITPR2"      "C3"         "STAMBPL1"  
##  [6] "GSTCD"      "FRMD6"      "ITGA9"      "TBC1D32"    "FRMD4A"    
## [11] "LRRC8C"     "ZMAT3"      "ATAD5"      "CA8"        "SLC9A9"    
## [16] "CACNB4"     "MEI4"       "SCIN"       "CLEC16A"    "LCP2"      
## [21] "PAG1"       "CTTNBP2"    "RFX3"       "RFX2"       "RASSF8"    
## [26] "ARHGAP22"   "PRAM1"      "WNT2B"      "GYPC"       "CSGALNACT1"
## [31] "DIXDC1"     "SH3RF1"     "DHRSX"      "PACS1"      "FADS3"     
## [1] "found 35 genes."

## [1] 28
##  [1] "PKD2L2"         "IL7"            "SGCE"           "MIR4435-2HG"   
##  [5] "GLIPR1L1"       "TTTY14"         "MCMDC2"         "EYS"           
##  [9] "RP1-225E12.2"   "RP5-1132H15.1"  "LANCL1-AS1"     "ITGA9-AS1"     
## [13] "RMDN2-AS1"      "LRIG2-DT"       "RP11-775D22.3"  "RP11-544A12.8" 
## [17] "RP11-506H20.1"  "RP11-1H15.2"    "RP11-867G2.8"   "RP11-571M6.7"  
## [21] "RP11-160E2.6"   "RP11-703M24.5"  "CEACAM16-AS1"   "KCNQ1OT1"      
## [25] "RP11-74J13.8"   "RP11-305E17.8"  "RP11-793H13.14" "RP1-18C9.3"    
## [29] "RP11-65F13.4"   "RP11-13J12.3"   "RP11-6G22.1"    "RP11-685G9.5"  
## [33] "RP11-555K12.4"  "RP11-617F9.2"   "ST3GAL1"        "SLC9A7"        
## [37] "PCDH11Y"        "APBB3"          "H1-10"          "RP11-37N22.1"  
## [41] "RP11-384C4.7"   "RP11-322M13.1" 
## [1] "found 11 genes."

## [1] 29
##  [1] "PLPP1"         "ACER3"         "SP140"         "CARMIL1"      
##  [5] "ZNF821"        "RCAN3"         "PLAGL1"        "SSPN"         
##  [9] "PUDP"          "SPATA6"        "TBC1D14"       "EPHB2"        
## [13] "ARHGAP20"      "SLC49A4"       "NKD1"          "WDPCP"        
## [17] "C11orf49"      "CD226"         "DENND2B"       "FGGY"         
## [21] "B3GNT5"        "PCED1B"        "SCFD2"         "FIRRE"        
## [25] "LINC02649"     "FTCDNL1"       "RP11-162D16.2" "RP11-202G18.1"
## [29] "RFX3-AS1"      "RP11-557H15.4" "LINC00884"     "LINC01184"    
## [33] "LINC02762"     "LINC02328"     "RP11-154H12.3" "TSIX"         
## [37] "RP11-323P17.2" "MIR223HG"      "RP11-419I17.1" "SEC14L1"      
## [1] "found 24 genes."

## [1] 30
##  [1] "HTR2B"        "TAGAP"        "PNMA3"        "TWIST2"       "NFIX"        
##  [6] "TNS1"         "RNF24"        "RNMT"         "BNIP3L"       "GYS1"        
## [11] "ARRDC2"       "GBE1"         "RLF"          "SPP1"         "IQSEC2"      
## [16] "SOX5"         "IQSEC1"       "SLC25A37"     "RIT2"         "AGPAT5"      
## [21] "MAPK13"       "SSBP3"        "ETS2"         "ABCG1"        "ABCA1"       
## [26] "DDIT4"        "SNTB2"        "CRADD"        "PPP1R3B"      "BNIP3"       
## [31] "FAM210A"      "CHST15"       "H1-0"         "RGL3"         "AC093818.1"  
## [36] "RP11-13N12.1" "FMNL1-DT"    
## [1] "found 34 genes."

## [1] 31
##  [1] "PDK4"          "NLRP1"         "CPED1"         "PEBP4"        
##  [5] "GPAT3"         "CFAP74"        "GASK1A"        "TENM4"        
##  [9] "SETBP1"        "C4orf19"       "DEPTOR"        "MIR31HG"      
## [13] "CYSLTR1"       "KCNQ3"         "RTN4RL1"       "CLEC9A"       
## [17] "LINC01285"     "RP11-131L23.1" "LINC01357"     "AC105760.2"   
## [21] "KIF9-AS1"      "HDAC2-AS2"     "HMGA1P4"       "MIR4300HG"    
## [25] "CTB-161M19.4"  "ZFPM2-AS1"     "LINC01301"     "RP11-946L16.1"
## [29] "RP11-187O7.3"  "MRC1"          "ATP6V0D1-DT"   "RP11-495L19.1"
## [33] "RP11-437L7.2"  "RP11-168F24.3" "RP11-4F5.3"    "KCNQ2"        
## [37] "HTR1E"         "KCNQ5"         "RP11-249L21.6"
## [1] "found 19 genes."

## [1] 32
##  [1] "TTC7A"                   "NIPAL2"                 
##  [3] "GAREM1"                  "SESN3"                  
##  [5] "PLXDC1"                  "HESX1"                  
##  [7] "NMNAT3"                  "LIPC"                   
##  [9] "PLD4"                    "CX3CR1"                 
## [11] "ACYP2"                   "ZDHHC14"                
## [13] "CATSPERE"                "SPATA13_ENSG00000182957"
## [15] "RNLS"                    "B3GLCT"                 
## [17] "AC003090.1"              "ENTPD3-AS1"             
## [19] "TMEM72-AS1"              "CTA-292E10.6"           
## [21] "TEX41"                   "LMCD1-AS1"              
## [23] "RP13-188A5.1"            "MIR646HG"               
## [25] "HCG22"                   "ZRANB2-AS2"             
## [27] "LINC01376"               "RNF217-AS1"             
## [29] "MEF2C-AS1"               "RP11-319G6.1"           
## [31] "RP11-381K20.2"           "RP11-692D12.1"          
## [33] "GMDS-DT"                 "RP11-679C8.2"           
## [35] "C8orf37-AS1"             "RP11-541P9.3"           
## [37] "RP11-511B23.2"           "LINC00907"              
## [39] "MIR222HG"                "RP11-111G13.1"          
## [41] "RP11-685G11.1"          
## [1] "found 15 genes."

## [1] 33
##  [1] "MUSK"         "ANGPT2"       "ECM2"         "FMO5"         "BCL2A1"      
##  [6] "ZDHHC19"      "BEAN1"        "GLYATL1"      "MOBP"         "RP11-621L6.2"
## [11] "SLC2A3"       "ABCA7"        "PLEKHH3"      "ANO8"         "RAP1GAP"     
## [16] "HIF3A"        "CHI3L1"       "BTG1"         "CEMIP2"       "HILPDA"      
## [21] "ADCY3"        "RGS16"        "TMEM140"      "ST18"         "PLIN2"       
## [26] "LYPD5"        "CCDC107"      "ANKZF1"       "NFIL3"        "ALDH1A1"     
## [31] "ADCY5"        "RBM44"        "CD55"         "ERO1A"        "SH3BGRL2"    
## [36] "STARD10"      "SLC12A8"      "HIF1A-AS3"   
## [1] "found 36 genes."

## [1] 34
##  [1] "ATP8B1"        "SLC5A9"        "SHOC1"         "ENO4"         
##  [5] "INSYN2B"       "ANKUB1"        "AC002463.3"    "ELMO1-AS1"    
##  [9] "TMLHE-AS1"     "AC096558.1"    "RP4-568F9.6"   "AC083884.8"   
## [13] "AC037445.1"    "CPB2-AS1"      "MYCBP2-AS1"    "DIAPH2-AS1"   
## [17] "CCDC200"       "AC018890.6"    "LINC01877"     "MEF2C-AS2"    
## [21] "CTD-2015H6.3"  "RHOQ-AS1"      "RP11-268P4.5"  "AP000487.6"   
## [25] "RP11-638I2.8"  "LINC02316"     "USP3-AS1"      "RP11-815J21.4"
## [29] "RP11-16B9.1"   "PRKCA-AS1"     "RP11-16C1.3"   "RP11-793A3.2" 
## [33] "RP11-58G13.1"  "RP1-256G22.2"  "CTD-2282P23.2" "DISC2"        
## [37] "RP11-314L11.1" "RP11-261A24.1" "RP11-1H15.4"   "RP11-1146N6.3"
## [41] "SLC26A7"      
## [1] "found 8 genes."

## [1] 35
##  [1] "HHAT"         "XAF1"         "FBXL13"       "PAQR3"        "LINC00624"   
##  [6] "MSR1"         "PDE8A"        "RGS1"         "DARS1"        "GTDC1"       
## [11] "SRGN"         "RGL1"         "MYO10"        "TNFAIP8"      "ARHGAP18"    
## [16] "RSU1"         "HTR7"         "ARID5B"       "NGLY1"        "ACSL1"       
## [21] "FRRS1"        "ACOT11"       "CDCP1"        "RHOBTB3"      "MARCHF8"     
## [26] "ALCAM"        "KLHL6"        "MFSD4B"       "TNFAIP8L3"    "MITF"        
## [31] "DPYD"         "PARVB"        "CTD-3088G3.8" "UBXN2B"       "PIK3IP1-DT"  
## [36] "MIR181A1HG"   "CTD-2643I7.5" "IFITM10"      "SBF2-AS1"    
## [1] "found 33 genes."

## [1] 36
##  [1] "CRYM"          "IGSF11"        "GLT1D1"        "TSBP1-AS1"    
##  [5] "KIF5C-AS1"     "MEIKIN"        "MTRNR2L8"      "PSMD7-DT"     
##  [9] "SYT7"          "COL5A3"        "IGSF9B"        "NALCN"        
## [13] "DNAH6"         "CHD5"          "CSMD2"         "CBLN2"        
## [17] "CFAP251"       "PDZRN4"        "STXBP6"        "CXXC5"        
## [21] "CADM2"         "SRRM3"         "ADGRB1"        "NRG3"         
## [25] "SLIT1"         "CR1L"          "RORB"          "FAM153CP"     
## [29] "BASP1-AS1"     "MIAT"          "TRHDE-AS1"     "RP11-259O2.1" 
## [33] "LINC01414"     "CTC-535M15.2"  "RP11-429A20.3" "RP11-368L12.1"
## [37] "LINC00558"     "U91319.1"      "RP11-436D23.1" "RP5-1015P16.1"
## [41] "RP11-335E8.3" 
## [1] "found 24 genes."

## [1] 37
##  [1] "ICA1"          "PRDM11"        "ST6GAL1"       "SLC26A4"      
##  [5] "PODXL2"        "AOPEP"         "LY96"          "SMIM14"       
##  [9] "PRMT9"         "GPR34"         "GAP43"         "CAPS2"        
## [13] "CDIN1"         "SRGAP3"        "CHSY3"         "C12orf75"     
## [17] "LINC00894"     "LINC01684"     "RP11-37B2.1"   "RP11-630C16.2"
## [21] "RP11-574F11.4" "STAB1"         "SESN1"         "TMED8"        
## [25] "IL27RA"        "NCOA7"         "FRMD4B"        "TMEM115"      
## [29] "CHSY1"         "SLC41A2"       "TLR2"          "DHRS3"        
## [33] "ROBO1"         "RNF150"        "LONRF3"        "TRNAU1AP"     
## [37] "TLR5"          "ZC3H6"        
## [1] "found 33 genes."

## [1] 38
##  [1] "CECR2"       "NME3"        "ABCC1"       "OGN"         "PLGRKT"     
##  [6] "IFIT3"       "IFIT2"       "CENPK"       "SAT1"        "RTN4IP1"    
## [11] "PCBD2"       "ITM2C"       "ERMN"        "TET1"        "LPAR6"      
## [16] "PTH2R"       "ADGRG5"      "FAM227B"     "RIC3"        "TLN2"       
## [21] "NAALADL2"    "ZFP36L1"     "IFIT1"       "DNAH14"      "ZNRF1"      
## [26] "CH17-55D9.1" "RP6-91H8.6"  "RP4-681L3.3" "ATP9A"       "RGCC"       
## [31] "TGFBI"       "ATP8B2"      "KIF5C"       "KLC2"        "MAMDC4"     
## [36] "IFNLR1"      "GK"         
## [1] "found 34 genes."

## [1] 39
##  [1] "PLEK"          "CYREN"         "RAB38"         "MMP24"        
##  [5] "OMD"           "TMEM241"       "IER3"          "AGBL3"        
##  [9] "NLGN4Y"        "CYTL1"         "IRAG1-AS1"     "H2AC20"       
## [13] "AC023590.1"    "ARHGAP26-AS1"  "ZNF451-AS1"    "AC105461.1"   
## [17] "ALG13-AS1"     "ARHGAP15-AS1"  "IPO9-AS1"      "RAP2C-AS1"    
## [21] "UFL1-AS1"      "RP11-528G1.2"  "FBXO30-DT"     "KDM4A-AS1"    
## [25] "BCL2L1-AS1"    "RP11-544A12.4" "DENND6A-AS1"   "ZBTB20-AS5"   
## [29] "GPRC5D-AS1"    "RP11-434H14.1" "LINC00639"     "RP11-106M3.3" 
## [33] "RNF213-AS1"    "H2BC7"         "RP11-121C2.3"  "RP11-19D22.1" 
## [37] "RP11-622I12.1" "RP11-458A7.1"  "RP11-21M24.6"  "RP11-314E10.1"
## [41] "RP11-399K19.1"
## [1] "found 12 genes."

## [1] 40
##  [1] "ANGPTL1"       "C11orf65"      "COL5A2"        "SPDYE2"       
##  [5] "MTCP1"         "RP11-321C24.1" "DOCK4-AS1"     "RP11-165F24.3"
##  [9] "AC017101.10"   "RP11-526K17.2" "RP11-575L7.8"  "RP1-117O3.2"  
## [13] "KCNMA1-AS1"    "LINC00960"     "RP11-712B9.2"  "ANK2-AS1"     
## [17] "CTD-2227I18.1" "LINC02742"     "RP11-39E3.3"   "CTD-3239E11.2"
## [21] "RP11-624C23.1" "RP11-463D19.1" "CTD-2537O9.1"  "RP11-493L12.3"
## [25] "RP11-713N11.4" "CTD-2647E9.3"  "RP11-317G6.1"  "RP11-516C1.1" 
## [29] "LMO7-AS1"      "RP11-66H6.3"   "LINC00621"     "RP11-737O24.2"
## [33] "TCF4-AS1"      "RP11-53B2.3"   "RP11-126O1.4"  "CTD-3149D2.4" 
## [37] "RP4-769N13.7"  "H2AC19"        "RP11-275G7.2"  "GS1-98E2.1"   
## [41] "RP1-80B9.4"    "CTD-2021K4.2" 
## [1] "found 6 genes."

Session information

gc()

##           used  (Mb) gc trigger  (Mb) limit (Mb) max used  (Mb)
## Ncells 4171674 222.8   10243768 547.1         NA 10243768 547.1
## Vcells 8967049  68.5   29538339 225.4      65536 29538339 225.4

sessionInfo()

## R version 4.2.3 (2023-03-15)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.4.1
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] stringr_1.5.0     limma_3.54.2      tidyr_1.3.0       ggpubr_0.6.0     
## [5] ggplot2_3.4.2     data.table_1.14.8
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_1.0.10            png_0.1-8              Biostrings_2.66.0     
##  [4] digest_0.6.31          utf8_1.2.3             R6_2.5.1              
##  [7] GenomeInfoDb_1.34.9    backports_1.4.1        stats4_4.2.3          
## [10] RSQLite_2.3.1          evaluate_0.20          httr_1.4.6            
## [13] pillar_1.9.0           zlibbioc_1.44.0        rlang_1.1.0           
## [16] rstudioapi_0.14        car_3.1-2              jquerylib_0.1.4       
## [19] blob_1.2.4             R.oo_1.25.0            R.utils_2.12.2        
## [22] S4Vectors_0.36.2       rmarkdown_2.21         labeling_0.4.2        
## [25] RCurl_1.98-1.12        bit_4.0.5              munsell_0.5.0         
## [28] broom_1.0.4            compiler_4.2.3         xfun_0.39             
## [31] pkgconfig_2.0.3        BiocGenerics_0.44.0    htmltools_0.5.5       
## [34] tidyselect_1.2.0       KEGGREST_1.38.0        GenomeInfoDbData_1.2.9
## [37] tibble_3.2.1           IRanges_2.32.0         fansi_1.0.4           
## [40] crayon_1.5.2           dplyr_1.1.2            withr_2.5.0           
## [43] R.methodsS3_1.8.2      bitops_1.0-7           grid_4.2.3            
## [46] jsonlite_1.8.4         gtable_0.3.3           lifecycle_1.0.3       
## [49] DBI_1.1.3              magrittr_2.0.3         scales_1.2.1          
## [52] cli_3.6.1              stringi_1.7.12         cachem_1.0.7          
## [55] carData_3.0-5          farver_2.1.1           XVector_0.38.0        
## [58] ggsignif_0.6.4         bslib_0.4.2            generics_0.1.3        
## [61] vctrs_0.6.2            RColorBrewer_1.1-3     org.Hs.eg.db_3.16.0   
## [64] tools_4.2.3            bit64_4.0.5            Biobase_2.58.0        
## [67] glue_1.6.2             purrr_1.0.1            abind_1.4-5           
## [70] fastmap_1.1.1          yaml_2.3.7             AnnotationDbi_1.60.2  
## [73] colorspace_2.1-0       rstatix_0.7.2          memoise_2.0.1         
## [76] knitr_1.44             sass_0.4.5